Conserved Protein Domain Family
TNRC6-PABC_bdg
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pfam16608: TNRC6-PABC_bdg (this model, PSSM-Id:293214 is obsolete and has been replaced by 465195)
TNRC6-PABC binding domain
TNRC6-PABC_bdg is a natively unstructured region on the higher eukaryote TNRC6 subset of GW182 proteins that carries the binding motif for the interaction with Polyadenylate-binding protein 1, PABC. TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localized to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay. Thus GW182 proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells being a major component of miRISCs. The interaction motif that binds to PABC is ShNWPPEFHPGVPWKGLQ. This region lies between a Q-rich region and the RRM, or RNA-recognition motif, pfam13893.
Links
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Statistics
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PSSM-Id: 293214
Aligned: 10 rows
Threshold Bit Score: 253.31
Created: 30-Jun-2015
Updated: 5-Aug-2015
Structure
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Aligned Rows:
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PubMed ReferencesClick to see Conserved Features Help
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
XP_006635522 1433 SPNSYSPYPLAGLNPNMNVSSIDVs--------GGL--S------MKDTsQSQSRLPQ-WThpNSMENLSGNSSPLEQNL 1495 spotted gar
XP_010158901  244 SPNTFAPYPLAGLNPNMNVNNMDIt--------GGL--S------VKDTsQSQSRLPQ-WThpNSMDNLSSAASSLDQNS 306  sunbittern
XP_004323088  118 lpdlqtkgPIPGYGSGFSSGGMDY---------GMV--G------GKEA-GTESRFKQ-WT--SMMEGL-PSVATQEANM 175  bottlenosed d...
XP_004778410 1515 PINAFSNFPI-GLNSNLNV-NMDM---------NSI----------KEP---QSRLRK-WT---TVDSISVNTS-LDQNS 1565 domestic ferret
XP_005468476 1501 dLHTKTPGMYSGLTPGSNLSGLEL---------GPMmgG------MKDLgGQQSRFK------WMMEGHSPAPSPPDSTI 1559 Nile tilapia
KKF27107     1457 SPNNYSPYSLSGLNPNMNVNCMEV---------GSL--S------MKEPpQPQSRLSQ-WThpHSIESLSGNSSPLEPNL 1518 large yellow ...
XP_008286959 1378 ALGSFSNFPL-SLNSNLNV-SLDMgv------gGGS--SgggavsYKEP--PQSRLKKlWA-----------TDPLEQN- 1433 bicolor damse...
XP_004071958 1384 plgplGNFPL-SLTPNLNV-PLDIavsggsssgGAV--T------YKEP--HQSRLKKlWA-----------TDILEQN- 1439 Japanese medaka
XP_006637326 1368 TLNSFSNFPI-GLNSNLNVSNLDI---------GSI--S------FKEP---QSRLKK-WT---ALD-ISVNP-SLDQNS 1420 spotted gar
XP_008121578 1572 QMSAFSNFPI-GSNSNLNV-NMDM---------GSM----------KEP---QSRLRK-WT---TVDSVSTNVPPLDQNA 1623 green anole

XP_006635522 1496 SKHG-----PSLGPpgk-ppmEDSYSPYNLIPSSESPASP-----LVAPDSWT-QGKASN--DKI-SNGTNINWPPEFCP 1560 spotted gar
XP_010158901  307 SKHGaipggLSIGPpgk-ssiDDSYGRYDLIQNSESPASPp----VAVPHSWS-RAKTDS--DKI-SNGSSINWPPEFHP 377  sunbittern
XP_004323088  176 HKNGaivapGKTRG-------GSPYNQFDIIPGDTLGGHT-----GPAGDSWL-PAKSPPtnKIG-SKSSNASWPPEFQP 241  bottlenosed d...
XP_004778410 1566 SKHGaissgFRLE--------ESPFVPYDFMNSSTSPASPp----GSIGDGWP-RAKSP-------NGSSSVNWPPEFRP 1625 domestic ferret
XP_005468476 1560 HKNGplpsaVKVRG-------GSPYSQYEMLGSDGLGI-Pp----QGSTDSWH-R--TPG--SKMgNKSATSSWPPEFQP 1622 Nile tilapia
KKF27107     1519 GKHGa-----NLGPpgkphqlEDSYSPYNLMSSSESPTSP-----LVPPDSWG-QGKSSS--DKM-ANGTNINWPPEFCP 1584 large yellow ...
XP_008286959 1434 SKPGamssgLRLE--------DSPF--YDFLSPGPSPLSPpgqsiGSVGDGWPpRANSPP------PHGNTVTWPPEFRP 1497 bicolor damse...
XP_004071958 1440 SKSGaissdLRLD--------DSPF--YDFLPPGPPPLSPpgqpiGSVGDGWPpRANSPP------SHANTVTWPPEFRP 1503 Japanese medaka
XP_006637326 1421 SKPGaipsgLRLE--------DSPFGPYDFMNTSNSPVSPp----GSVGDGWPnRAKSP-------HGSSNVNWPPEFRP 1481 spotted gar
XP_008121578 1624 SKNGaisggFRLE--------EASFVPYDFMNGSNSPASPp----GPIGEGWS-RAKSP-------SGSSSVNWPPEFRP 1683 green anole

XP_006635522 1561 GVPWKGLQNI-DPETDPNVTPGSVPSGPTIN-TnIQDVNRYLLRDRSGGssPPPSQNGALPSADAW-PVSA--HT--SSF 1633 spotted gar
XP_010158901  378 GVPWKGLQNI-DPENDPDVTPGSVPTGPTINtT-IQDVNRYLLKSGGSS--PTSSQNATLPSSSAW-PLSA--SGysSSF 450  sunbittern
XP_004323088  242 GVPWKGIQNI-DPESDPYVTPGSVLGGTATS-P-IVDTDHQLLRDNTTG--SNSSLNTSLPSPGAW-PYSA--Sd--NSF 311  bottlenosed d...
XP_004778410 1626 GEPWKGYPNI-DPETDPYVTPGSVINNLSIN-T-VREVDH--LRDRNSG--SSSSLNTTLPSTSAWsSIRA--SNynVPL 1696 domestic ferret
XP_005468476 1623 GVPWKGIQNSgDPESDPYMTPGSVLGSPGSP-S-LNDSDHQLLRDNI-G--PNPSLNTSLPSPGAW-PYSA--Sd--SPL 1692 Nile tilapia
KKF27107     1585 GVPWKGLQNI-DPETDPNVTPGSVPSGPTIN-TnIQDVNRYLLRDRSGGssPTSSQNEALPPSTDW-PVSG--YT--SSF 1657 large yellow ...
XP_008286959 1498 GEPWKGYPNI-DPETDPYVTPGSVINNLSIN-T-VRDTDH--LRDRNNG--PSSSLNTTMPSNSAWsSIRAssHS--GSL 1568 bicolor damse...
XP_004071958 1504 GEPWKGYPNI-DPETDPYVTPGSVINNLSIN-T-VRDTDH--LRDRNNG--PPSSLNTTMPSNSAWsSIRAssHS--GSL 1574 Japanese medaka
XP_006637326 1482 GEPWKGYPNI-DPETDPYVTPGSVINNLSIN-T-VRDVDH--LRDRNNG--STSSLNTTLPSTSAWsSIRAsnYS--GSL 1552 spotted gar
XP_008121578 1684 GEPWKGYPNI-DPETDPYITPGSVTNNLSIN-T-VREADH--LRDRNGG--SSSSLNTALPSTSAWsSIRAsnYN--VSL 1754 green anole

XP_006635522 1634 SLSPSATdsAGKLSD-MKSTWSP----GPISHTQASLSHELWKVpqgPR--NTTAPTRPPPGLTNTKL--S---STWSGS 1701 spotted gar
XP_010158901  451 SSIASAPsiAGKLSD-IKSTWSS----GPISHTQASLSHELWKV---PR--NTTAPTRPPPGLTNTKP--S---STWGAS 515  sunbittern
XP_004323088  312 SNVHS-T--SAKFPD-YKSTWSP----DPIGHNPTHLSNKMWKNhisSR--NTTPLPRPPPGLTNPKP--S---SPWSST 376  bottlenosed d...
XP_004778410 1697 SSTAQST--SARNSD-SKLTWSP----G--SVTNTSLAHELWKVplpPK--NITAPSRPPPGLTGQKP--Pl--STWDNS 1761 domestic ferret
XP_005468476 1693 SNPHS----TGKYSD-YKPSWPP----EPIGQ------NKLWKt---SR--NSSQLPRPPPGLTNQKQasP---SPWGTG 1749 Nile tilapia
KKF27107     1658 SLSSPETddAGKLSE-MKSTWSP----GPISHSQASLSHELWKVpqgPRs-SNTAPSRPPPGLTNTKP--S---STWGGN 1726 large yellow ...
XP_008286959 1569 TSTAQST--SARPSE-SK--WSP----SGGSVSNSSLAHELWKVplpPKalSVAAPSRPPPGLTSQKP--SsasSGWDGS 1637 bicolor damse...
XP_004071958 1575 TSTAQST--SARPSE-SK--WSP----GGGSVSNSSLAHELWKVpltPKalPVAAPSRPPPGLTSQKP------SGWDSS 1639 Japanese medaka
XP_006637326 1553 SSTAQST--SARNSD-SKstWSP------GPVTNTSLAHELWKVplpPK--GITAPSRPPPGLTGQKP--P---SSWDNS 1616 spotted gar
XP_008121578 1755 SSTAQSTs-SARNSDsSKPTWSTasanGGSSGSSTSLAHELWKVplpPK--SVAAPSRPPPGLTGQKG--Pl--SSWENP 1827 green anole

XP_006635522 1702 ALgl------vpGWS-------SSYSSGTtwsTDSSGRT 1727 spotted gar
XP_010158901  516 PL----------GWTss----ySSGSAWS---TDSSGRT 537  sunbittern
XP_004323088  377 APrs------vrGWGtq----dSRLASAStwsDGGSVRp 405  bottlenosed dolphin
XP_004778410 1762 PLrv------ggGWGns----dARYTPGCswgESSSGRI 1790 domestic ferret
XP_005468476 1750 GPrl------arSWGggginqeSRFGQGSawsDGAASRG 1782 Nile tilapia
KKF27107     1727 SLgl------aqGWS-------SSYTTGTtwsTDSSTRT 1752 large yellow croaker
XP_008286959 1638 ALrl-------gGWGst----eSRYTPgsswgdssssgr 1665 bicolor damselfish
XP_004071958 1640 ALrr-------gGWGft----eSRYTPGSswgDGSSSGR 1667 Japanese medaka
XP_006637326 1617 SLrl------ggGWGss----dSRYTPGSswgDNSSGRT 1645 spotted gar
XP_008121578 1828 LQrfgggggggaGWSas----eGRYTPGSawgESSSGRI 1862 green anole
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